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cartography
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
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Create supplemental table of sequence accessions and authors
#67
huddlej
closed
8 months ago
0
Create supplemental table of all cluster-specific mutations
#66
huddlej
closed
8 months ago
0
Within between stats
#65
huddlej
closed
8 months ago
1
Revisit how to create mutation tables for HA/NA analysis
#64
huddlej
closed
9 months ago
0
Write results text for simulated populations
#63
huddlej
closed
10 months ago
0
Quantify ability of SARS-CoV-2 embeddings to capture recombinant lineages relative to parental lineages
#62
huddlej
closed
10 months ago
1
Recalculate generations per year for simulated coronavirus populations
#61
huddlej
closed
10 months ago
1
Outline tables and figures
#60
huddlej
closed
6 months ago
0
Refine the SARS-CoV-2 recombinant dataset to include parental lineages of recombinants
#59
huddlej
closed
11 months ago
0
Recalculate optimal flu cluster parameters without A2/re clade assignment
#58
huddlej
closed
11 months ago
1
Refine the SARS-CoV-2 recombinant dataset to include parental lineages of recombinants
#57
huddlej
closed
11 months ago
0
Use new pathogen-embed interface to embed alignments and tune HDBSCAN hyperparameters
#56
huddlej
closed
1 year ago
0
Refine abstract
#55
huddlej
closed
8 months ago
0
Pin dependencies in Conda environment to stable versions
#54
huddlej
closed
1 year ago
1
Calculate within and between clade/cluster genetic distances per embedding and clade definition
#53
nandsra21
closed
9 months ago
2
Submit to PLoS Computational Biology
#52
huddlej
closed
4 months ago
0
Submit to bioRxiv
#51
huddlej
closed
5 months ago
0
Incorporate feedback from Trevor/Alli
#50
huddlej
closed
5 months ago
0
Prepare social media thread about the project
#49
huddlej
opened
1 year ago
0
Update interactive figures on paper’s website
#48
huddlej
closed
5 months ago
0
Send paper to Trevor and Alli for review
#47
huddlej
closed
5 months ago
0
Write abstract for Epidemics
#46
huddlej
closed
1 year ago
1
Write discussion
#45
huddlej
closed
8 months ago
0
Finish intro
#44
huddlej
closed
10 months ago
2
Finish methods
#43
huddlej
closed
10 months ago
1
Write results for SARS-CoV-2
#42
huddlej
closed
9 months ago
0
Tune figures for SARS-CoV-2
#41
huddlej
closed
10 months ago
1
Write results text for H3N2 HA/NA
#40
huddlej
closed
9 months ago
1
Tune figures for H3N2 HA/NA
#39
huddlej
closed
10 months ago
1
Write results text for H3N2 HA
#38
huddlej
closed
9 months ago
1
Tune figures
#37
huddlej
closed
5 months ago
5
Tune HDBSCAN parameters
#36
huddlej
closed
1 year ago
1
Calculate variation of information (VI) between groups of tips with known clade labels and clusters
#35
huddlej
closed
1 year ago
1
Create Docker image for the analysis
#34
huddlej
opened
1 year ago
2
Create separate commands for embedding, clustering, and distance matrix creation
#33
huddlej
closed
1 year ago
2
Move pathogen-embed into its own repository
#32
huddlej
closed
1 year ago
1
Drop low- and high-recombination coronavirus-like simulations
#31
huddlej
closed
1 year ago
0
Drop Zika and MERS from the analysis
#30
huddlej
closed
1 year ago
0
Outline paper
#29
huddlej
closed
5 months ago
0
Optimize parameters with simulations and cross-validation
#28
huddlej
closed
1 year ago
0
Use variation of information
#27
huddlej
closed
1 year ago
0
adding indel tests to hamming distance method
#26
huddlej
closed
1 year ago
2
Cluster specific mutations
#25
huddlej
closed
1 year ago
1
Refine scatterplot aesthetics
#24
huddlej
closed
1 year ago
0
Add simulations
#23
huddlej
closed
1 year ago
0
Implement unified workflow
#22
huddlej
closed
2 years ago
0
Using MCC from TreeKnit
#21
nandsra21
closed
2 years ago
2
Calculating hamming distance requires uppercase fasta
#20
cassiawag
closed
2 years ago
1
Update main README to add developers section
#19
nandsra21
closed
2 years ago
1
Add all gridsearch figures to main github
#18
nandsra21
closed
2 years ago
0
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